MolNFT v1 · #115330 · protein

Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator 3-chloro-5-[6-(5-fluoropyridin-2-YL)PYRIMIDIN-4- YL]BENZONITRILE - (HTL14242)

5CGD · Metabotropic glutamate receptor 5,ENDOLYSIN,METABOTROPIC…: “Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with…”. X-ray diffraction, 2 ligands (OLA, 51E), 2 pockets (best…

PDB: 5CGD
Type: protein
Length: 408 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metabotropic glutamate receptor 5,ENDOLYSIN,METABOTROPIC glutamate receptor 5
EC: 3.2.1.17
UniProt: P41594, P00720
Ligands: OLA, 51E
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 73% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metabotropic glutamate receptor 5,ENDOLYSIN,METABOTROPIC glutamate receptor 5 (EC 3.2.1.17)	protein	408	73% helix, 3% strand	P41594, P00720

Ligands and binding sites

OLA · Oleic acid · ligand · 4 copies · chains A
51E · 3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	264	0.80	0.92	45	51E
2	440	0.68	0.80	45	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5CGD · Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane… · the same entry in another collection · chain A against A, TM-score 1.00
P41594 · AlphaFold monomer V2.0 prediction for metabotropic glutamate receptor 5 (P41594) · a predicted model of the same protein · chain A against A, TM-score 0.58

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P41594
Every structure of UniProt P00720
Elsewhere: RCSB PDB 5CGD · PDBe 5CGD · UniProt P41594 · UniProt P00720

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